def test_positive_on_AFE(self):
"""
[]------[]
[]------[]
"""
self.graph.add_path(["start", str(self.ex1), str(self.ex2), "end"])
self.transcripts = [[str(self.ex1), str(self.ex2)]]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_negative_one_path_one_exon(self):
"""
[]<------[]
"""
path = ["end", str(self.ex1), str(self.ex2), "start"]
path.reverse()
self.graph.add_path(path)
self.transcripts = [path]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_positive_no_AFE_with_ALE(self):
"""
[]--------->[]--------->[]
[]--------->[]----->[]
"""
path1 = ["start", str(self.ex1), str(self.ex5), str(self.ex3), "end"]
path2 = ["start", str(self.ex1), str(self.ex5), str(self.ex2), "end"]
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_positive_two_path_one_exon(self):
"""
[]------->[]
[]---->[]
"""
path1 = ["start", str(self.ex1), str(self.ex2), "end"]
path2 = ["start", str(self.ex5), str(self.ex2), "end"]
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])
def test_positive_two_path_two_exon(self):
"""
[]------------>[]---------->[]
[*]--->[*]-->[]---------->[]
"""
self.ex6 = Exon("chrX", 7000, 8000, "ex1.1", "+")
self.exonsDB[str(self.ex6)] = self.ex6
path1 = ["start", str(self.ex1), str(self.ex3), str(self.ex6), "end"]
path2 = ["start", str(self.ex5), str(self.ex2), str(self.ex3), str(self.ex6), "end"]
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 3])
def test_negative_no_AFE_with_ALE(self):
"""
[]<-----[]<----[]<-----[]
[]<---------[]<-----[]
"""
path1 = ["end", str(self.ex4), str(self.ex1), str(self.ex2), str(self.ex3), "start"]
path2 = ["end", str(self.ex5), str(self.ex2), str(self.ex3), "start"]
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 0)
def test_negative_two_path_one_exon(self):
"""
[]<-------[]
[]<-------------[]
"""
path1 = ["end", str(self.ex1), str(self.ex2), "start"]
path2 = ["end", str(self.ex1), str(self.ex3), "start"]
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])
def test_negative_single_AFE_with_ALE(self):
"""
[]<-------[]<-------[]
[]<----[]<----------[*]
"""
self.ex6 = Exon("chrX", 7000, 8000, "ex1.1", "-")
self.exonsDB[str(self.ex6)] = self.ex6
path1 = ["end", str(self.ex1), str(self.ex2), str(self.ex3), "start"]
path2 = ["end", str(self.ex4), str(self.ex2), str(self.ex6), "start"]
path1.reverse()
path2.reverse()
self.graph.add_path(path1)
self.graph.add_path(path2)
self.transcripts = [path1, path2]
paths = list(find_AFE(self.graph, self.exonsDB, self.transcripts))
self.assertEqual(len(paths[0]), 2)
self.assertItemsEqual(get_num_exons(paths), [2, 2])